Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= TCDB::G3LHY8 (358 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 161 bits (408), Expect = 2e-44 Identities = 102/339 (30%), Positives = 167/339 (49%), Gaps = 9/339 (2%) Query: 1 MLELRNAAKMVGADYHIYPTDLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHF 60 +L L N +K + + +L ++ G +LGP+ GKT+++RL+AG ++P G I Sbjct: 6 ILTLSNISKRFASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILL 65 Query: 61 DGTDVTGMPVQKRNVAMVYQQFINYPALTVYNNIASPMRISGKDAATIDREVRKAAELLK 120 +G D+ +P +KR V+Q + +P LTV++N+A ++++G D I V A +++ Sbjct: 66 NGDDIARIPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVR 125 Query: 121 LTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPKIFAQ 180 L+ + R P LSGGQ+QR A+ARA+V ++L+DE L+ LDYKLR++++ EL ++ Q Sbjct: 126 LSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQ 185 Query: 181 SGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPPLNTL 240 G FVY T + EAL + ++ G+ Q G E+Y P NL A + +N Sbjct: 186 LGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIGE--INVF 243 Query: 241 D---VTKSGNVFTRPS--GVTIPVPSHLAVVPDGPVTIAFHPHHLGL--APQTGDAARLQ 293 D V G S GV + V + P L + P + Sbjct: 244 DGEIVQALGEYQYEASINGVVREIRCDHRFAVGDKVHVMLRPEDLRIDCRPDVAERKGFP 303 Query: 294 ARTLVSEITGSESFVHLEYDGVRWVMLAHGIHDIDPDME 332 L TG H+E + + +M + DPD + Sbjct: 304 GIVLERSYTGQTLNSHIELENGQTLMAHEFFDEDDPDFD 342 Lambda K H 0.319 0.136 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 276 Number of extensions: 13 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 358 Length of database: 369 Length adjustment: 29 Effective length of query: 329 Effective length of database: 340 Effective search space: 111860 Effective search space used: 111860 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory